LAMMPS (2 Apr 2025 - Development - d4867ab55e-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
  using 1 OpenMP thread(s) per MPI task
# GJ thermostat

units   	metal
atom_style      full

boundary 	p p p
read_data argon.lmp
Reading data file ...
  orthogonal box = (0 0 0) to (32.146 32.146 32.146)
  1 by 2 by 2 MPI processor grid
  reading atoms ...
  864 atoms
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     0 = max # of 1-2 neighbors
     0 = max # of 1-3 neighbors
     0 = max # of 1-4 neighbors
     1 = max # of special neighbors
  special bonds CPU = 0.002 seconds
  read_data CPU = 0.015 seconds
include ff-argon.lmp
#############################
#Atoms types - mass - charge#
#############################
#@ 1 atom types #!THIS LINE IS NECESSARY DON'T SPEND HOURS FINDING THAT OUT!#

variable Ar equal 1

#############
#Atom Masses#
#############

mass ${Ar}      39.903
mass 1      39.903

###########################
#Pair Potentials - Tersoff#
###########################

pair_style      lj/cubic
pair_coeff      * * 0.0102701 3.42


velocity all create 10 2357 mom yes dist gaussian
neighbor 1 bin

timestep 0.1

compute myKE all ke
compute myPE all pe

fix lang all gjf 10 10 1 26488 vel vfull method 1

run 5000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- GJ methods: doi:10.1080/00268976.2019.1662506

@Article{gronbech-jensen_complete_2020,
title = {Complete set of stochastic Verlet-type thermostats for correct Langevin simulations},
volume = {118},
number = {8},
url = {https://www.tandfonline.com/doi/full/10.1080/00268976.2019.1662506},
doi = {10.1080/00268976.2019.1662506},
journal = {Molecular Physics},
author = {Grønbech-Jensen, Niels},
year = {2020}
}

- GJ-I vfull method: doi:10.1080/00268976.2012.760055

@Article{gronbech-jensen_simple_2013,
title = {A simple and effective Verlet-type algorithm for simulating Langevin dynamics},
volume = {111},
url = {http://www.tandfonline.com/doi/abs/10.1080/00268976.2012.760055},
doi = {10.1080/00268976.2012.760055},
pages = {983-991},
number = {8},
journal = {Molecular Physics},
author = {Grønbech-Jensen, Niels and Farago, Oded},
year = {2013}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 6.9407173
  ghost atom cutoff = 6.9407173
  binsize = 3.4703587, bins = 10 10 10
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cubic, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.427 | 6.427 | 6.427 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   10            -56.207652      0             -55.092137      33.341103    
      5000   7.946377      -55.076514      0             -54.190084      337.31999    
Loop time of 2.0998 on 4 procs for 5000 steps with 864 atoms

Performance: 20573.405 ns/day, 0.001 hours/ns, 2381.181 timesteps/s, 2.057 Matom-step/s
65.2% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.53641    | 0.54389    | 0.54721    |   0.6 | 25.90
Bond    | 0.00056487 | 0.0006195  | 0.00068462 |   0.0 |  0.03
Neigh   | 0.10567    | 0.1086     | 0.11128    |   0.7 |  5.17
Comm    | 0.96913    | 0.97758    | 0.98191    |   0.5 | 46.56
Output  | 0.00025213 | 0.00025642 | 0.00026405 |   0.0 |  0.01
Modify  | 0.25061    | 0.25105    | 0.25172    |   0.1 | 11.96
Other   |            | 0.2178     |            |       | 10.37

Nlocal:            216 ave         216 max         216 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost:         884.75 ave         885 max         884 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs:           4536 ave        4737 max        4335 min
Histogram: 2 0 0 0 0 0 0 0 0 2

Total # of neighbors = 18144
Ave neighs/atom = 21
Ave special neighs/atom = 0
Neighbor list builds = 273
Dangerous builds = 0

fix energies all ave/time 1 20000 20000 c_myKE c_myPE #file ave.out

thermo 2000
run 35000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 6.428 | 6.428 | 6.428 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
      5000   7.946377      -55.076514      0             -54.190084      337.31999    
      6000   8.2565866     -55.129244      0             -54.208209      324.57967    
      8000   7.9942397     -55.101417      0             -54.209648      331.24127    
     10000   8.5413968     -55.083292      0             -54.130486      337.82599    
     12000   8.3682078     -55.090905      0             -54.157419      335.08066    
     14000   8.5082065     -55.085051      0             -54.135948      336.2765     
     16000   8.1944037     -55.090733      0             -54.176635      334.03786    
     18000   8.2607106     -55.030131      0             -54.108637      352.49892    
     20000   8.1154691     -55.104072      0             -54.198779      330.14203    
     22000   8.5592601     -55.152019      0             -54.197221      318.03507    
     24000   8.3182914     -55.115242      0             -54.187324      328.46084    
     26000   8.3691375     -55.125275      0             -54.191685      325.43673    
     28000   8.531632      -55.107097      0             -54.155381      331.42771    
     30000   8.1102222     -55.099011      0             -54.194304      332.04678    
     32000   8.5558571     -55.077016      0             -54.122598      339.87746    
     34000   8.4213946     -55.097068      0             -54.157649      333.34935    
     36000   8.0936615     -55.152202      0             -54.249342      316.20169    
     38000   7.999652      -55.048407      0             -54.156034      345.07945    
     40000   8.6699753     -55.087634      0             -54.120485      337.23709    
Loop time of 17.6726 on 4 procs for 35000 steps with 864 atoms

Performance: 17111.263 ns/day, 0.001 hours/ns, 1980.470 timesteps/s, 1.711 Matom-step/s
65.4% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 5.0739     | 5.1178     | 5.1689     |   1.5 | 28.96
Bond    | 0.0043764  | 0.004688   | 0.0051706  |   0.4 |  0.03
Neigh   | 0.83797    | 0.85506    | 0.87554    |   1.8 |  4.84
Comm    | 6.816      | 6.8932     | 6.9215     |   1.7 | 39.00
Output  | 0.0043624  | 0.0045336  | 0.004998   |   0.4 |  0.03
Modify  | 3.3008     | 3.3033     | 3.3066     |   0.1 | 18.69
Other   |            | 1.494      |            |       |  8.45

Nlocal:            216 ave         222 max         210 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost:          905.5 ave         911 max         899 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Neighs:        4535.75 ave        4837 max        4218 min
Histogram: 1 0 0 1 0 0 1 0 0 1

Total # of neighbors = 18143
Ave neighs/atom = 20.998843
Ave special neighs/atom = 0
Neighbor list builds = 2140
Dangerous builds = 0
Total wall time: 0:00:19
